Contacts of the strand formed by residues 150 - 155 (chain F) in PDB entry 3LUE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D MET* 1.3 90.6 - - - +
149F THR* 1.3 62.3 - - - +
151F ILE* 1.3 56.1 + - - -
165F ILE 2.9 16.0 + - - -
292F ASP 4.5 0.2 - - - -
293F LEU* 3.0 22.4 - - - +
296F ASN* 3.4 11.4 - - - -
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Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D MET* 2.9 1.5 - - - +
150F GLY* 1.3 73.6 - - - +
152F VAL* 1.3 74.0 + - - +
162F THR* 4.3 6.7 - - + -
163F VAL 3.2 20.4 - - - +
164F PRO* 4.0 15.0 - - + -
278F THR* 4.0 21.1 - - + +
281F SER* 3.7 29.8 - - - -
282F ILE* 4.3 12.6 - - + -
293F LEU* 3.4 33.0 - - + +
296F ASN 2.9 5.9 + - - +
297F THR* 3.4 12.7 - - + +
298F VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 3.0 15.5 - - + +
138F ALA* 3.5 23.6 - - + +
142F LEU* 2.1 51.8 - - + -
151F ILE* 1.3 78.4 - - - +
153F MET* 1.3 63.2 + - - +
154F ASP 3.9 0.4 - - - -
161F HIS 3.7 1.1 - - - +
162F THR* 3.4 4.5 - - - -
163F VAL* 3.2 32.0 + - + +
165F ILE* 4.7 1.3 - - + -
298F VAL* 3.2 11.0 - - + +
300F SER* 3.5 27.1 - - - +
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Residues in contact with MET 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE* 5.9 0.2 - - + -
152F VAL* 1.3 74.9 - - - +
154F ASP* 1.3 61.4 + - - +
155F SER* 3.9 4.7 + - - -
160F THR* 3.5 29.6 - - + -
161F HIS 3.5 2.7 - - - -
162F THR* 3.6 8.5 - - + -
261F LEU* 6.5 0.4 - - + -
274F ILE* 3.5 25.1 - - + -
278F THR* 3.5 25.4 - - + +
297F THR* 5.5 4.3 - - + -
298F VAL 2.8 13.6 + - - +
299F LEU* 3.5 17.7 - - + -
300F SER 2.9 22.8 + - - +
304F THR* 4.0 17.4 - - + +
309F ILE* 5.3 6.3 - - + -
313F MET* 3.8 20.0 - - + -
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Residues in contact with ASP 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F PRO* 3.7 10.3 - - + +
137F GLN* 2.9 18.3 - - - +
138F ALA* 1.5 71.9 + - + +
141F SER* 3.4 1.6 + - - -
153F MET* 1.3 72.3 - - - +
155F SER* 1.3 61.8 + - - +
156F GLY 4.5 2.4 + - - -
159F VAL 3.6 1.2 - - - +
160F THR* 3.1 24.9 - - - -
161F HIS 2.9 11.3 + - - +
300F SER* 2.6 20.9 + - - +
301F GLY* 4.9 2.5 - - - -
339F VAL* 4.4 0.7 - - - +
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Residues in contact with SER 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F MET* 3.9 6.5 + - - -
154F ASP* 1.3 72.4 + - - +
156F GLY* 1.3 61.4 + - - +
159F VAL 3.7 2.9 - - - -
160F THR* 2.9 24.8 + - - +
181F ALA* 4.2 3.8 - - - -
261F LEU* 4.4 6.0 - - - +
300F SER 3.0 10.3 + - - -
301F GLY* 3.3 12.5 - - - -
303F THR* 3.0 49.2 + - - +
304F THR* 4.2 13.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il